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- Issue 2: Remove examples from unexported .plot_embedding_base - Issue 3: Replace all \dontrun with \donttest (18 occurrences, 8 files) - Issue 4: Rewrite install_optional_dependencies to be informational-only - Add GEDI_set_verbose C++ export to fix train() double-run bug - Fix train() splitting iterations into 1 + (n-1) separate calls - Suppress C++ verbose output when R verbose=1 (progress bar mode) - Fix plot_convergence faceted layout rbind column mismatch - Add testthat infrastructure with 83 tests across 7 test files - Regenerate all man pages
…SeuratObject::pbmc_small` and `gedi2`, and refine H5AD reader error messages.
…erbose output, and updated documentation examples.
…eGEDIObject` parameters, add a publication reference, and perform minor code formatting.
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